Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. - Ying Wang; Noushin Ghaffari; Charles D. Johnson; Ulisses M. Braga-Neto; Hui Wang; Rui Chen; Huaijun Zhou (BMC Bioinform., 2011)

OBGene: Optimal barcode generator for NGS experiments. - Esmaeil Atashpaz-Gargari; Mohammad Shahrokh Esfahani; Richard Metz; Charles D. Johnson (GENSiPS, 2012)

Fast DNA barcode generating algorithm using Radix Coding method. - Amir Nikooienejad; Richard Metz; Byung-Jun Yoon; Charles D. Johnson (GENSiPS, 2012)

Modeling the Next Generation Sequencing sample processing pipeline for the purposes of classification. - Noushin Ghaffari; Mohammadmahdi R. Yousefi; Charles D. Johnson; Ivan Ivanov 001; Edward R. Dougherty (BMC Bioinform., 2013)

De novo transcriptome assemblies and annotation for pacifie whiteleg shrimp. - Noushin Ghaffari; Osama A. Arshad; Hyundoo Jeong; John Thiltges; Michael F. Criscitiello; Byung-Jun Yoon; Aniruddha Datta; Charles D. Johnson (GlobalSIP, 2014)

Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data. - Noushin Ghaffari; Jordi Abante; Raminder Singh; Philip D. Blood; Charles D. Johnson (XSEDE, 2016)

Examining De Novo Transcriptome Assemblies via a Quality Assessment Pipeline. - Noushin Ghaffari; Osama A. Arshad; Hyundoo Jeong; John Thiltges; Michael F. Criscitiello; Byung-Jun Yoon; Aniruddha Datta; Charles D. Johnson (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)